1IY7

Crystal Structure of CPA and sulfamide-based inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Sulfamide-Based Inhibitors for Carboxypeptidase A. Novel Type Transition State Analogue Inhibitors for Zinc Proteases

Park, J.D.Kim, D.H.Kim, S.J.Woo, J.R.Ryu, S.E.

(2002) J.Med.Chem. 45: 5295-5302


  • PubMed Abstract: 
  • N-Sulfamoylphenylalanine and its derivatives having varied alkyl groups on the terminal amino group were designed rationally as transition state analogue inhibitors for carboxypeptidase A (CPA) and synthesized. In CPA inhibitory assays the parent com ...

    N-Sulfamoylphenylalanine and its derivatives having varied alkyl groups on the terminal amino group were designed rationally as transition state analogue inhibitors for carboxypeptidase A (CPA) and synthesized. In CPA inhibitory assays the parent compound having the (S)-configuration, i.e., (S)-1a, showed potent inhibitory activity with the K(i) value of 0.64 microM. Its enantiomer was shown to be much less potent (K(i) = 470 microM). Introduction of an alkyl group such as methyl or isopropyl group on the terminal amino group of (S)-1a lowered the inhibitory potency drastically. Introduction of a methyl group on the internal amino group of (S)-1a also caused a drastic reduction of the inhibitory activity. The structure of the CPA x(S)-1a complex determined by single-crystal X-ray diffraction reveals that the sulfamoyl moiety interacts with the zinc ion and functional groups at the active site of CPA, which is reminiscent of the postulated stabilization mode of a tetrahedral transition state in the CPA-catalyzed hydrolysis of a peptide substrate. On the basis of the design rationale and the binding mode of (S)-1a to CPA shown by X-ray crystallographic analysis, the present inhibitors are inferred to be a novel type of transition state analogue inhibitor for CPA.


    Organizational Affiliation

    Center for Integrated Molecular Systems, Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31 Hyoja-dong, Namku, Pohang 790-784 Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase A
A
307Bos taurusGene Names: CPA1 (CPA)
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to Gene View: CPA1
Go to UniProtKB:  P00730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CXA
Query on CXA

Download SDF File 
Download CCD File 
A
PHENYLALANINE-N-SULFONAMIDE
C9 H12 N2 O4 S
PHGMHLLGXKQIDY-QMMMGPOBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CXAKi: 650 nM (97) BINDINGDB
CXAKi: 650 nM BINDINGMOAD
CXAKi: 640 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.688α = 90.00
b = 60.467β = 82.55
c = 47.256γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
SCALAdata scaling
CCP4data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance